Bio::S...ullHit(3pm)

🌸 Bio::S...ullHit — the manual page bestie 💖

okay so this is the docs for Bio::S...ullHit(3pm), straight out of the User Contributed Perl Documentation collection. no cap, it's giving "niche but iconic". let's go 💅

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✨ NAME ✨

Bio::Search::Hit::BlastPullHit — a parser and hit object for BLASTN hits 🧬✨

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🦋 SYNOPSIS 🦋

# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                                        -file   => 'result.blast');

while (my $result = $in->next_result) {
            while (my $hit = $result->next_hit) {
                    print $hit->name, "\n";
                    print $hit->score, "\n";
                    print $hit->significance, "\n";

                    while (my $hsp = $hit->next_hsp) {
                            # process HSPI objects
                    }
            }
}

like… look at that nesting. she's structured, she's committed, she's literally the blueprint 🫶

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💜 DESCRIPTION 💜

This object implements a parser for BLASTN hit output. that's the whole vibe check — it parses, it hits, it serves. 👑

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🎀 FEEDBACK 🎀

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. fr fr, they want to hear from you 🥺

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. like, respectfully, slide into the group chat not the DMs 🙈 Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. receipts help everybody bestie ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR — Sendu Bala 👑

Email bix@sendu.me.uk

the main character, honestly 💖

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🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here

(no for real, that's what it says — the placeholder is still placeholding 😭)

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⭐ APPENDIX ⭐

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, underscore means "not for you, bestie" 🔒

🍓 new

• Title: new
• Usage: my $obj = Bio::Search::Hit::BlastNHit->new();
• Function: Builds a new Bio::Search::Hit::BlastNHit object.
• Returns: Bio::Search::Hit::BlastNHit
• Args:

-chunk    => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent   => Bio::PullParserI object (required if no -chunk)
-hit_data => array ref with [name description score significance]

where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
hit, and $start and $end define the tell() position within the
filehandle that the hit data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)

so yeah — give her a -chunk or give her a -parent, one of the two, that's the rule 🫶 and those $start/$end positions are the tell() coordinates, but they're optional and will just default to the whole entire thing the filehandle is describing. convenient? yes. iconic? also yes. 💅

🧚 next_hsp

• Title: next_hsp
• Usage: while( $hsp = $obj->next_hsp()) { ... }
• Function: Returns the next available High Scoring Pair
• Example: (there isn't one, bestie, it's just empty here 🙈)
• Returns: Bio::Search::HSP::HSPI object or null if finished
• Args: none

🌸 hsps

• Usage: $hit_object->hsps();
• Purpose: Get a list containing all HSP objects.
• Example: @hsps = $hit_object->hsps();
• Returns: list of Bio::Search::HSP::BlastHSP objects.
• Argument: none

💖 hsp

• Usage: $hit_object->hsp( [string] );
• Purpose: Get a single HSPI object for the present HitI object.
• Example:

$hspObj  = $hit_object->hsp;  # same as 'best'
$hspObj  = $hit_object->hsp('best');
$hspObj  = $hit_object->hsp('worst');

• Returns: Object reference for a Bio::Search::HSP::HSPI object.
• Argument: String (or no argument).
  • No argument (default) = highest scoring HSP (same as 'best').
  • 'best' = highest scoring HSP.
  • 'worst' = lowest scoring HSP.
• Throws: Exception if an unrecognized argument is used. 🚨

See Also: hsps(), num_hsps()

🦄 rewind

• Title: rewind
• Usage: $result->rewind;
• Function: Allow one to reset the HSP iterator to the beginning, so that next_hsp() will subsequently return the first hsp and so on.
• Returns: n/a
• Args: none

rewind is the "let's run that back" button of the whole operation, and honestly? we love a second chance arc 🔥

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perl v5.32.1 · 2021-08-15 — that's the source/version and date bestie, the official receipts 🧾✨ and with that, this page is done. slay, stay parsed, and may all your hits be significant 💅💖🦋